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jupyter Python R

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The source code is available at sayalaruano/cv.

Last updated on 2022-03-21.

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Sebastián Ayala-Ruano

I am a focused and motivated young researcher that has worked in Bioinformatics and Cheminformatics for four years at different laboratories. My current interests are devoted to Network Science, Complex Systems, and Machine Learning for drug discovery. Moreover, I am involved in various initiatives to empower Bioinformatics in Ecuador and Latin America.

Education

B.Eng., Biotechnology

Universidad San Francisco de Quito (USFQ)

Quito, Ecuador

2020 - 2016

  • Minor: Systems engineering.
  • GPA: 3.78/4 (Magna Cum Laude) - second best score of the College of Biological and Environmental Sciences 2020 class.

Research Experience

Applied Signal Processing and Machine Learning Research Group - USFQ

Research Assistant

Quito, Ecuador

2021

  • Created a method based on network science and similarity searching to explore the chemical space of antiparasitic peptides and discover new drugs (See details here).
  • Advisors: Yovani Marrero-Ponce, Noel Pérez Pérez

Computational and Theoretical Chemistry Group - USFQ

Undergraduate Researcher

Quito, Ecuador

2020 - 2017

  • Identified binding specificity between repressor proteins and a transcriptional factor associated with the jasmonic acid pathway in Arabidopsis thaliana through molecular dynamics simulations and machine learning algorithms (See details here).
  • Advisor: Miguel Angel Méndez Silva

Bio-Chemoinformatics Group - Universidad de Las Américas

Research Intern

Quito, Ecuador

2020 - 2018

  • Understood the impact of horizontal gene transfer in the genome of Streptomyces clavuligerus using phylogenetics, and other bioinformatics tools (See details here).
  • Proposed molecular mimicry between Zika envelope protein and human neuronal proteins through molecular dynamics and protein-protein interaction networks.
  • Advisors: Vinicio Armijos, Yunierkis Perez

Tumor Metabolism and Therapeutic Oncology Laboratory - Gwangju Institute of Science and Technology

Research Intern

Gwangju, South Korea

2019

  • Performed density functional theory and molecular dynamics simulations to understand the impact of a mutation in the ZN domain of the CRBN protein (See details here).
  • I continued working on this research project in my undergraduate thesis, and now we are in the process of publishing these results in a scientific article.
  • Advisors: Miguel Angel Méndez Silva, Steve K. Cho

Teaching Experience

Linux and Bash/AWK scripting Boot Camp

RSG Ecuador and iGEM Ecuador

Virtual event

2021

  • Co-organizer and co-instructor. I designed and taught most of the course material.
  • This course covered the basics of Linux, terminal usage, text and file processing command line tools, Bash/AWK scripting with applications in Bioinformatics, and Git/GitHub.

Undergraduate Teaching Assistant

Learning Center - USFQ

Virtual events

2020

  • Provided online mentorship of Biotechnology, Mathematics, and Systems Engineering subjects to undergraduate students that needed help.

Undergraduate Teaching Assistant

General Biology Laboratory - USFQ

Quito, Ecuador

2018 - 2016

  • Graded reports, tests, and other homework from the course.
  • Provided feedback and guidance to undergraduate students in topics of the course.

Publications

  1. Ayala-Ruano S., Marrero-Ponce Y., Aguilera‑Mendoza L., Pérez N., Agüero-Chapin G., Antunes A., Aguilar A. (2021). Exploring the Chemical Space of Antiparasitic Peptides and Discovery of New Promising Leads through a Novel Approach based on Network Science and Similarity Searching. ChemRxiv [Preprint]. doi: doi.org/10.33774/chemrxiv-2021-tgv69.
  2. Castillo-Vilcahuaman, C., Valdivia C., Osorio-Mogollón C., Silva-Andrade, C., Puche, R., Ayala‐Ruano, S., Cuesta-Astroz, Y., Parra, G (2020). 4th ISCB Latin American Student Council Symposium: a virtual and inclusive experience during COVID19 times. F1000Research, 9. doi: 10.12688/f1000research.28330.1.
  3. Oña-Chuquimarca, S., Ayala-Ruano, S., Goossens, Pauwels, L., Goossens, A., Leon-Reyes, A., & Méndez, M. A (2020). The molecular basis of JAZ-MYC coupling, a protein-protein interface essential for plant response to stressors. Frontiers in Plant Science, 11, 1139. doi: 10.3389/fpls.2020.01139. This article was included in the Frontiers in Plant Science 2020 highlights e-book. doi: 10.3389/978-2-88966-723-9.
  4. Ayala‐Ruano, S., Santander‐Gordón, D., Tejera, E., Perez‐Castillo, Y., & Armijos-Jaramillo, V. (2019). A putative antimicrobial peptide from Hymenoptera in the megaplasmid pSCL4 of Streptomyces clavuligerus ATCC 27064 reveals a singular case of horizontal gene transfer with potential applications. Ecology and Evolution, 9 (5), 2602-2614. doi: 10.1002/ece3.4924.

Conference presentations

  1. The molecular basis of JAZ-MYC coupling, a protein-protein interface essential for plant response to stressors. (2021). Oral presentation. 6th Brazilian Student Council Symposium: Omics and Data Science (See details here).
  2. Modeling of protein-protein interaction and search for key residues by machine learning of the JAZ-MYC3 complex of Arabidopsis thaliana. (2020). Oral presentation. 5th RSG-Argentine Symposium of Young Researchers in Bioinformatics (See details here).
  3. In silico detection of horizontal gene transfer in Streptomyces clavuligerus. (2020). Oral presentation. International Society for Computational Biology Student Council Webinar series (See details here).
  4. In silico detection of an antimicrobial peptide (AMP) transferred horizontally from arthropods to bacteria. (2019). Oral presentation. 2nd RSG-Colombia Symposium (See details here).
  5. Modeling of Protein-protein interaction and search for key residues by machine learning of a protein complex in the jasmonic acid route in Arabidopsis thaliana. (2019). Poster presentation. XLIII National Biology Conference (See details here).
  6. Structural changes due to a mutation in Cereblon might be a cause for intellectual disability. (2019). Poster presentation. Global Intern Program - Gwangju Institute of Science and Technology (See details here).

Honors and Awards

Best oral presentation award

6th Brazilian Student Council Symposium: Omics and Data Science

Virtual event

2021

Innovation challenge For more data on labor informality award

Datalat, PNUD Ecuador, UN Women Ecuador, and the International Labour Organization

Virtual event

2021

  • This competition searched for a technological solution to collect labor informality data in Ecuador. There were 39 proposals from 80 interdisciplinary teams (See details about the challenge here).

Chancellor’s Honor List

Universidad San Francisco de Quito

Quito, Ecuador

2020 - 2016

  • This award recognizes students who have a GPA of 3.7/4 or higher.

Third HPC Summer School Colombia: Bio and Data Science scholarship

CyberColombia

Virtual event

2020

  • The scholarship covered registration expenses for the event.

2nd RSG-Colombia Symposium travel award

RSG Colombia

Ibagué, Colombia

2019

  • This award covered the travel expenses to attend the event.

Global Intern Program

Gwangju Institute of Science and Technology

Gwangju, South Korea

2019

  • The GIP awarded students with accommodation and a monthly stipend to cover living expenses for eight weeks. During this time, we were involved in a research project and received valuable training and mentoring.

Leadership and Service

Regional Student Group (RSG) Ecuador

International Society for Computational Biology Student Council

Quito, Ecuador

Current - 2020

HerrCompBioinfo

Regional Student Group Ecuador and Open Life Science (OLS) program

Virtual event

2021

  • Created an open-source educational resource of computational tools for Bioinformatics enthusiasts written in Spanish.
  • During the OLS program, I learned how to create and manage open science and open source projects.

Saturdays.AI Quito 2021 project leader

Saturdays.AI Quito

Virtual event

2021

  • Led my group project, which was an early plant disease detector based on convolutional neural networks, trained to recognize two types of maize infectious diseases.(See details here).

Note: I have developed other personal projects related to data science, machine learning, drug discovery, and other topics (See details here).